I am trying to analyse some single cell RNA seq data with MAST, currently I'm using an edgeR pipeline and I cannot work out how to properly test a contrast in MAST.

The experimental setup is a 3x2 with 3 strains and 2 conditions, I'd like to test differential expression between the conditions within each strain. I have set up a "strain-condition" style factor for my samples and I'm using a `~0 + group` design. My understanding was that I could use

zlm_output <- zlm(~0 + group, x)

summary_contr <- summary(zlm_output, doLRT = c(1, -1, 0, 0, 0, 0))

To test my contrast of interest. However this gives me the following error

Error in logFC(zlmfit, contrast0, contrast1) :
Assuming comparision to intercept, but I can't figure out what coefficient that corresponds to. Provide `contrast0`.

Could someone guide me in the correct usage of this package for testing contrasts?

You can fit such a model a "cellmean model" (zlm_cellmean = zlm(~ 0 + group, x)) though it is possibly a little less statistically efficient [1] than using contrasts that explicitly includes an intercept:

Can you be more specific when you say "interface for contrasts" The contrasts(colData(x)$strain) = "contr.sum" business is base R and determines the coding for your factors, hence interpretation of your coefficients. Venables & Ripley is the canonical reference for that.

Specifying linear combinations of coefficients to test is documented in ?"ZlmFit-class".